Uneven chromosome contraction and expansion in the maize genome

Rémy Bruggmann, Arvind K. Bharti, Heidrun Gundlach, Jinsheng Lai, Sarah Young, Ana C. Pontaroli, Fusheng Wei, Georg Haberer, Galina Fuks, Chunguang Du, Christina Raymond, Matt C. Estep, Renyi Liu, Jeffrey L. Bennetzen, Agnes P. Chan, Pablo D. Rabinowicz, John Quackenbush, W. Brad Barbazuk, Rod A. Wing, Bruce BirrenChad Nusbaum, Steve Rounsley, Klaus F.X. Mayer, Joachim Messing

Research output: Contribution to journalArticle

94 Citations (Scopus)

Abstract

Maize (Zea mays or corn), both a major food source and an important cytogenetic model, evolved from a tetraploid that arose about 4.8 million years ago (Mya). As a result, maize has extensive duplicated regions within its genome. We have sequenced the two copies of one such region, generating 7.8 Mb of sequence spanning 17.4 cM of the short arm of chromosome 1 and 6.6 Mb (25.6 cM) from the long arm of chromosome 9. Rice, which did not undergo a similar whole genome duplication event, has only one orthologous region (4.9 Mb) on the short arm of chromosome 3, and can be used as reference for the maize homoeologous regions. Alignment of the three regions allowed identification of syntenic blocks, and indicated that the maize regions have undergone differential contraction in genic and intergenic regions and expansion by the insertion of retrotransposable elements. Approximately 9% of the predicted genes in each duplicated region are completely missing in the rice genome, and almost 20% have moved to other genomic locations. Predicted genes within these regions tend to be larger in maize than in rice, primarily because of the presence of predicted genes in maize with larger introns. Interestingly, the general gene methylation patterns in the maize homoeologous regions do not appear to have changed with contraction or expansion of their chromosomes. In addition, no differences in methylation of single genes and tandemly repeated gene copies have been detected. These results, therefore, provide new insights into the diploidization of polyploid species.

Original languageEnglish
Pages (from-to)1241-1251
Number of pages11
JournalGenome Research
Volume16
Issue number10
DOIs
StatePublished - 10 Oct 2006

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Zea mays
Chromosomes
Genome
Genes
Methylation
Chromosomes, Human, Pair 9
Intergenic DNA
Chromosomes, Human, Pair 3
Polyploidy
Tetraploidy
Chromosomes, Human, Pair 1
Cytogenetics
Introns
Food
Oryza

Cite this

Bruggmann, R., Bharti, A. K., Gundlach, H., Lai, J., Young, S., Pontaroli, A. C., ... Messing, J. (2006). Uneven chromosome contraction and expansion in the maize genome. Genome Research, 16(10), 1241-1251. https://doi.org/10.1101/gr.5338906
Bruggmann, Rémy ; Bharti, Arvind K. ; Gundlach, Heidrun ; Lai, Jinsheng ; Young, Sarah ; Pontaroli, Ana C. ; Wei, Fusheng ; Haberer, Georg ; Fuks, Galina ; Du, Chunguang ; Raymond, Christina ; Estep, Matt C. ; Liu, Renyi ; Bennetzen, Jeffrey L. ; Chan, Agnes P. ; Rabinowicz, Pablo D. ; Quackenbush, John ; Barbazuk, W. Brad ; Wing, Rod A. ; Birren, Bruce ; Nusbaum, Chad ; Rounsley, Steve ; Mayer, Klaus F.X. ; Messing, Joachim. / Uneven chromosome contraction and expansion in the maize genome. In: Genome Research. 2006 ; Vol. 16, No. 10. pp. 1241-1251.
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Bruggmann, R, Bharti, AK, Gundlach, H, Lai, J, Young, S, Pontaroli, AC, Wei, F, Haberer, G, Fuks, G, Du, C, Raymond, C, Estep, MC, Liu, R, Bennetzen, JL, Chan, AP, Rabinowicz, PD, Quackenbush, J, Barbazuk, WB, Wing, RA, Birren, B, Nusbaum, C, Rounsley, S, Mayer, KFX & Messing, J 2006, 'Uneven chromosome contraction and expansion in the maize genome', Genome Research, vol. 16, no. 10, pp. 1241-1251. https://doi.org/10.1101/gr.5338906

Uneven chromosome contraction and expansion in the maize genome. / Bruggmann, Rémy; Bharti, Arvind K.; Gundlach, Heidrun; Lai, Jinsheng; Young, Sarah; Pontaroli, Ana C.; Wei, Fusheng; Haberer, Georg; Fuks, Galina; Du, Chunguang; Raymond, Christina; Estep, Matt C.; Liu, Renyi; Bennetzen, Jeffrey L.; Chan, Agnes P.; Rabinowicz, Pablo D.; Quackenbush, John; Barbazuk, W. Brad; Wing, Rod A.; Birren, Bruce; Nusbaum, Chad; Rounsley, Steve; Mayer, Klaus F.X.; Messing, Joachim.

In: Genome Research, Vol. 16, No. 10, 10.10.2006, p. 1241-1251.

Research output: Contribution to journalArticle

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AU - Du, Chunguang

AU - Raymond, Christina

AU - Estep, Matt C.

AU - Liu, Renyi

AU - Bennetzen, Jeffrey L.

AU - Chan, Agnes P.

AU - Rabinowicz, Pablo D.

AU - Quackenbush, John

AU - Barbazuk, W. Brad

AU - Wing, Rod A.

AU - Birren, Bruce

AU - Nusbaum, Chad

AU - Rounsley, Steve

AU - Mayer, Klaus F.X.

AU - Messing, Joachim

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Bruggmann R, Bharti AK, Gundlach H, Lai J, Young S, Pontaroli AC et al. Uneven chromosome contraction and expansion in the maize genome. Genome Research. 2006 Oct 10;16(10):1241-1251. https://doi.org/10.1101/gr.5338906